The following are the best secondary schools in South Sudan
- Comboni Comprehensive Secondary School in Kajo-Keji county of Central Equatoria state
- St. Bakhita Secondary school in Eastern Equatoria state
- Magwi secondary School
- Marialbai Secondary school of Western Bahr el Ghazal
- Fulla Secondary School of County of Eastern Equatoria state
- Loa Secondary school of Magwi County